1. Nope, we like to kill off the noobs so all safety mechanisms are100% disabled
Seriously though, you say you swapped the ports, what do you mean by that, did you swap the pins you asigned or physically swap wires around?
2. Jog controls are the arrow keys or are you meaning the flyout screen when you press the Tab key? If the arrow keys are not working then you have possibly deleted or asigned different hotkeys to the axis. If you go to the Config menu then down to hotkeys you can asign them by clciking on for example X++ and when the press a key box pops up press the right arrow on the keyboard.
3. Check that when you command a positive X move the tool travels right in relation to your work(table moves to left), same for a positive Y , tool will be away from you in relation to the work (table towards you) If an axis is moving the wrong way then you can tick the reverse axis box in Homing and Limits, again from the Config menu.
Hood